Metabolomics-based analysis of the diatom Cheatoceros tenuissimus combining NMR and GC-MS techniques.

Metabolomics, a recent addition to omics sciences, studies small molecules across plants, animals, humans, and marine organisms. Nuclear magnetic resonance (NMR) and gas chromatography-mass spectrometry (GC-MS) are widely used in those studies, including microalgae metabolomics. NMR is non-destructive and highly reproducible but has limited sensitivity, which could be supplemented by joining GC-MS analysis. Extracting metabolites from macromolecules requires optimization for trustworthy results. Different extraction methods yield distinct profiles, emphasizing the need for optimization. The results indicated that the optimized extraction procedure successfully identified NMR and GC-MS-based metabolites in MeOH, CHCl3, and H2O extraction solvents. The findings represented the spectral information related to carbohydrates, organic molecules, and amino acids from the water-soluble metabolites fraction and a series of fatty acid chains, lipids, and sterols from the lipid fraction. Our study underscores the benefit of combining NMR and GC-MS techniques to comprehensively understand microalgae metabolomes, including high and low metabolite concentrations and abundances.•In this study, we focused on optimizing the extraction procedure and combining NMR and GC-MS techniques to overcome the low NMR sensitivity and the different detected range limits of NMR and GC-MS.•We explored metabolome diversity in a tropical strain of the small cells' diatom Cheatoceros tenuissimus.

Isolation and Bioactivity Evaluation of Sesquiterpenes from an Alcyonarian of the Genus Lemnalia from the Saudi Arabian Red Sea.

Over the last decades, soft corals have been proven a rich source of biologically active compounds, featuring a wide range of chemical structures. Herein, we investigated the chemistry of an alcyonarian of the genus Lemnalia (Neptheidae), specimens of which were collected from the coral reefs near Al Lith, on the south-west coast of Saudi Arabia. A series of chromatographic separations led to the isolation of 31 sesquiterpenes, featuring mainly the nardosinane and neolemnane carbon skeletons, among which three (13, 14 and 28) are new natural products. The metabolites isolated in sufficient amounts were evaluated in vitro in human tumor and non-cancerous cell lines for a number of biological activities, including their cytotoxic, anti-inflammatory, anti-angiogenic, and neuroprotective activities, as well as for their effect on androgen receptor (AR)-regulated transcription. Among the tested metabolites, compound 12 showed comparable neuroprotective activity to the positive control N-acetylcysteine, albeit at a 10-fold lower concentration.

Marine picoplankton metagenomes and MAGs from eleven vertical profiles obtained by the Malaspina Expedition.

The Ocean microbiome has a crucial role in Earth's biogeochemical cycles. During the last decade, global cruises such as Tara Oceans and the Malaspina Expedition have expanded our understanding of the diversity and genetic repertoire of marine microbes. Nevertheless, there are still knowledge gaps regarding their diversity patterns throughout depth gradients ranging from the surface to the deep ocean. Here we present a dataset of 76 microbial metagenomes (MProfile) of the picoplankton size fraction (0.2-3.0 µm) collected in 11 vertical profiles covering contrasting ocean regions sampled during the Malaspina Expedition circumnavigation (7 depths, from surface to 4,000 m deep). The MProfile dataset produced 1.66 Tbp of raw DNA sequences from which we derived: 17.4 million genes clustered at 95% sequence similarity (M-GeneDB-VP), 2,672 metagenome-assembled genomes (MAGs) of Archaea and Bacteria (Malaspina-VP-MAGs), and over 100,000 viral genomic sequences. This dataset will be a valuable resource for exploring the functional and taxonomic connectivity between the photic and bathypelagic tropical and sub-tropical ocean, while increasing our general knowledge of the Ocean microbiome.

Influence of global warming and industrialization on coral reefs: A 600-year record of elemental changes in the Eastern Red Sea.

The Red Sea has been recognized as a coral reef refugia, but it is vulnerable to warming and pollution. Here we investigated the spatial and temporal trends of 15 element concentrations in 9 coral reef sediment cores (aged from the 1460s to the 1980s AD) to study the influence of global warming and industrialization on the Eastern Red Sea coral reefs. We found Na, Ca, Cr, Fe, Co, Ni, and Sr concentrations were higher in the northern Red Sea (i.e., Yanbu), whereas Mg, P, S, Mn, and Cd concentrations were higher in the southern Red Sea (i.e., Thuwal & Al Lith) reef sediments. In the central (i.e., Thuwal) to southern (i.e., Al Lith) Red Sea, the study revealed diverse temporal trends in element concentrations. However, both reef sedimentation rates (-36.4 % and -80.5 %, respectively) and elemental accumulation rates (-49.4 % for Cd to -12.2 % for Zn in Thuwal, and -86.2 % for Co to -61.4 % for Cu in Al Lith) exhibited a declining pattern over time, possibly attributed to warming-induced thermal bleaching. In the central to northern Red Sea (i.e., Yanbu), the severity of thermal bleaching is low, while the reef sedimentation rates (187 %), element concentrations (6.7 % for S to 764 % for Co; except Na, Mg, Ca, Sr, and Cd), and all elemental accumulation rates (190 % for Mg to 2697 % for Co) exponentially increased from the 1970s, probably due the rapid industrialization in Yanbu. Our study also observed increased trace metal concentrations (e.g., Cu, Zn, and Ni) in the Thuwal and Al Lith coral reefs with severe bleaching histories, consistent with previous reports that trace metals might result in decreased resistance of corals to thermal stress under warming scenarios. Our study points to the urgent need to reduce the local discharge of trace metal pollutants to protect this biodiversity hotspot.

Design and use of a new primer pair for the characterization of the cyanobacteria Synechococcus and Prochlorococcus communities targeting petB gene through metabarcoding approaches.

During the last years, the application of next-generation sequencing (NGS) technologies to search for specific genetic markers has become a crucial method for the characterization of microbial communities. Illumina MiSeq, likely the most widespread NGS platform for metabarcoding experiments and taxonomic classification, allows processing shorter reads than the classical SANGER sequencing method and therefore requires specific primer pairs that produce shorter amplicons. Specifically, for the analysis of the commonly studied Prochlorococcus and Synechococcus communities, the petB marker gene has recently stood out as able to provide deep coverage to determine the microdiversity of the community. However, current petB primer set produce a 597 bp amplicon that is not suitable for MiSeq chemistry. Here, we designed and tested a petB primer pair that targets both Prochlorococcus and Synechococcus communities producing an appropriate amplicon to be used with state-of-the-art Illumina MiSeq. This new primer set allows the classification of both groups to a low taxonomic level and is therefore suitable for high throughput experiments using MiSeq technologies, therefore constituting a useful, novel tool to facilitate further studies on Prochlorococcus and Synechococcus communities. •This work describes the de novo design of a Prochlorococcus and Synechococcus-specific petB primer pair, allowing the characterization of both populations to a low taxonomic level.•This primer pair is suitable for widespread Illumina MiSeq sequencing technologies.•petB was confirmed as an adequate target for the characterization of both picocyanobacteria.

Global biogeography of the smallest plankton across ocean depths.

Tiny ocean plankton (picoplankton) are fundamental for the functioning of the biosphere, but the ecological mechanisms shaping their biogeography were partially understood. Comprehending whether these microorganisms are structured by niche versus neutral processes is relevant in the context of global change. We investigate the ecological processes (selection, dispersal, and drift) structuring global-ocean picoplanktonic communities inhabiting the epipelagic (0 to 200 meters), mesopelagic (200 to 1000 meters), and bathypelagic (1000 to 4000 meters) zones. We found that selection decreased, while dispersal limitation increased with depth, possibly due to differences in habitat heterogeneity and dispersal barriers such as water masses and bottom topography. Picoplankton ß-diversity positively correlated with environmental heterogeneity and water mass variability, but this relationship tended to be weaker for eukaryotes than for prokaryotes. Community patterns were more pronounced in the Mediterranean Sea, probably because of its cross-basin environmental heterogeneity and deep-water isolation. We conclude that different combinations of ecological mechanisms shape the biogeography of the ocean microbiome across depths.

Top abundant deep ocean heterotrophic bacteria can be retrieved by cultivation.

Traditional culture techniques usually retrieve a small fraction of the marine microbial diversity, which mainly belong to the so-called rare biosphere. However, this paradigm has not been fully tested at a broad scale, especially in the deep ocean. Here, we examined the fraction of heterotrophic bacterial communities in photic and deep ocean layers that could be recovered by culture-dependent techniques at a large scale. We compared 16S rRNA gene sequences from a collection of 2003 cultured heterotrophic marine bacteria with global 16S rRNA metabarcoding datasets (16S TAGs) covering surface, mesopelagic and bathypelagic ocean samples that included 16 of the 23 samples used for isolation. These global datasets represent 60 322 unique 16S amplicon sequence variants (ASVs). Our results reveal a significantly higher proportion of isolates identical to ASVs in deeper ocean layers reaching up to 28% of the 16S TAGs of the bathypelagic microbial communities, which included the isolation of 3 of the top 10 most abundant 16S ASVs in the global bathypelagic ocean, related to the genera Sulfitobacter, Halomonas and Erythrobacter. These isolates contributed differently to the prokaryotic communities across different plankton size fractions, recruiting between 38% in the free-living fraction (0.2-0.8 µm) and up to 45% in the largest particles (20-200 µm) in the bathypelagic ocean. Our findings support the hypothesis that sinking particles in the bathypelagic act as resource-rich habitats, suitable for the growth of heterotrophic bacteria with a copiotroph lifestyle that can be cultured, and that these cultivable bacteria can also thrive as free-living bacteria.

Carbon sequestration potential of transplanted mangroves and exotic saltmarsh plants in the sediments of subtropical wetlands.

Coastal blue carbon ecosystems offer promising benefits for both climate change mitigation and adaptation. While there have been widespread efforts to transplant mangroves from the tropics to the subtropics and to introduce exotic saltmarsh plants like Spartina alterniflora in China, few studies have thoroughly quantified the chronological records of carbon sequestration with different organic carbon (OC) sources. To understand how variations in OC sources can affect the carbon sequestration potential of coastal wetland environment over time, we conducted a study on typical islands with two scenarios: S. alterniflora invasion and mangrove transplantation. Our study determined chronological records of carbon sequestration and storage from five sediment profiles and traced changes in the OC sources using carbon stable isotope (δ13C) and C:N ratios in response to these scenarios. The S. alterniflora invasion resulted in an 84 ± 19 % increase in the OC burial rate compared to unvegetated mudflats, while mangrove transplantation resulted in a 167 ± 74 % increase in the OC burial rate compared to unvegetated mudflats. S. alterniflora and mangroves showed greater carbon sequestration potential in areas with high supplies of suspended particulate matter, while mangroves needed to grow to a certain scale to display obvious carbon sequestration benefits. In the mangrove saltmarsh ecotone, mature mangrove habitats exhibited resistance to the S. alterniflora invasion, while mangrove transplantation in the environment invaded by S. alterniflora had a significant effect on OC contribution. Besides, plant-derived OC can be exported to the surrounding environment due to the rapid turnover of sediments. The blue carbon chronosequence-based estimation of OC sources and burial rates provides a useful reference for establishing carbon accounting policies.

Tracking the early signals of crude oil in seawater and plankton after a major oil spill in the Red Sea.

Understanding the immediate impacts of oil spills is essential to recognizing their long-term consequences on the marine environment. In this study, we traced the early (within one week) signals of crude oil in seawater and plankton after a major oil spill in October 2019 in the Red Sea. At the time of sampling, the plume had moved eastward, but we detected significant signs of incorporation of oil carbon into the dissolved organic carbon pool, resulting in a 10-20% increase in the ultraviolet (UV) absorption coefficient (a254) of chromophoric dissolved organic matter (CDOM), elevated oil fluorescence emissions, and depletion of the carbon isotope composition (δ13C) of the seawater. The abundance of the picophytoplankton Synechococcus was not affected, but the proportion of low nucleic acid (LNA) bacteria was significantly higher. Moreover, specific bacterial genera (Alcanivorax, Salinisphaera, and Oleibacter) were enriched in the seawater microbiome. Metagenome-assembled genomes (MAGs) suggested that such bacteria presented pathways for growing on oil hydrocarbons. Traces of polycyclic aromatic hydrocarbons (PAHs) were also detected in zooplankton tissues, revealing the rapid entry of oil pollutants into the pelagic food web. Our study emphasizes the early signs of short-lived spills as an important aspect of the prediction of long-term impacts of marine oil spills.

Abiotic selection of microbial genome size in the global ocean.

Strong purifying selection is considered a major evolutionary force behind small microbial genomes in the resource-poor photic ocean. However, very little is currently known about how the size of prokaryotic genomes evolves in the global ocean and whether patterns reflect shifts in resource availability in the epipelagic and relatively stable deep-sea environmental conditions. Using 364 marine microbial metagenomes, we investigate how the average genome size of uncultured planktonic prokaryotes varies across the tropical and polar oceans to the hadal realm. We find that genome size is highest in the perennially cold polar ocean, reflecting elongation of coding genes and gene dosage effects due to duplications in the interior ocean microbiome. Moreover, the rate of change in genome size due to temperature is 16-fold higher than with depth up to 200 m. Our results demonstrate how environmental factors can influence marine microbial genome size selection and ecological strategies of the microbiome.

Contrasting sensitivity among oligotrophic marine microbial communities to priority PAHs.

Oligotrophic areas represent a large proportion of the oceans, wherein microbial food webs largely determine carbon flux dynamics and biogeochemical cycles. However, little is known regarding the sensitivity of microbial planktonic communities to pollutants in such areas. Organic pollutants such as polycyclic aromatic hydrocarbons (PAH/s) are toxic oil derivatives that occur as complex mixtures and reach marine environments through different sources. Therefore, our study analyzed the PAH tolerance of natural photosynthetic and heterotrophic bacteria and eukaryotes from the oligotrophic Red Sea, which is uniquely susceptible to high oil contamination. Natural communities sampled from the surface layer were exposed to a concentration gradient of a mixture of 16 priority PAHs at in situ conditions for 48 h. The populations of the dominant picocyanobacteria Synechococcus sp., picophytoeukaryotes, and low nucleic acid (LNA) bacteria decreased upon exposure to PAHs in a strong dose-dependent manner. Chlorophyll-a, which was measured as an indicator of the total autotrophic community response, also decreased substantially. High nucleic acid (HNA) bacteria, however, exhibited lower growth inhibition (<50%). The lethal concentration (LC10) thresholds to the 16-PAH mixture demonstrated contrasting sensitivities among the microbial communities studied increasing from picoeukaryotes (5.98 ± 2.08 µg L-1) < chlorophyll-a (19.51 ± 8.11 µg L-1) < LNA bacteria (23.63 ± 10.64 µg L-1) < Synechococcus sp. (26.77 ± 13.34 µg L-1) < HNA bacteria (97.13 ± 17.28 µg L-1). The sensitivity of Red Sea Synechococcus and picophytoeukaryotes to the 16-PAH mixture was between 2 and 6.5 times higher compared to single PAH compounds tested previously. However, some populations of HNA bacteria and Synechococcus sp., were highly tolerant, suggesting an adaptation to chronic pollution. Concerningly, the LC10 toxicity thresholds approached the ambient PAH concentrations in the Red Sea, suggesting that environmental oil pollution actively shapes the microbial community structures in the region.

Rapid evolution of SARS-CoV-2 challenges human defenses.

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.

Underestimated PAH accumulation potential of blue carbon vegetation: Evidence from sedimentary records of saltmarsh and mangrove in Yueqing Bay, China.

Sediments of blue carbon vegetation are becoming a sink of natural and anthropogenic pollutants, such as polycyclic aromatic hydrocarbons (PAHs). However, the extent to which PAHs are accumulated and varied in blue carbon sediments, and the impact of blue carbon vegetation on the accumulation and retention capacity of PAHs, have been poorly explored. This study examines the sedimentary records of PAHs in profiles from mangrove plantation, saltmarsh, and mudflat in Ximen Island and Maoyan Island of Yueqing Bay, China. The existence of blue carbon vegetation provides a sheltered environment for the accelerated burial of sediment and OC. Decadal PAH sedimentation records show staged changes characterized by the emission of PAHs and colonization of blue carbon vegetation, reflecting the accelerated burial of PAHs in sediments by blue carbon vegetation colonization. In addition, the colonization of blue carbon vegetation contributes to the shift of PAH compositions in sediments. This study provides new insights into the underestimated PAH accumulation potential and retention capacity of blue carbon vegetation and the corresponding underlying sediments, supporting the environmental benefits of blue carbon vegetation.

Food-chain length determines the level of phenanthrene bioaccumulation in corals.

Exposure from the dissolved-phase and through food-chains contributes to bioaccumulation of polycyclic aromatic hydrocarbons (PAHs) in organisms such as fishes and copepods. However, very few studies have investigated the accumulation of PAHs in corals. Information on dietary uptake contribution to PAHs accumulation in corals is especially limited. Here, we used Cavity-Ring-Down Spectroscopy (CRDS) to investigate the uptake rates and accumulation of a 13C-labeled PAH, phenanthrene, in Acropora millepora corals over 14 days. Our experiment involved three treatments representing exposure levels of increasing food-chain length. In Level W, corals were exposed to 13C-phenanthrene directly dissolved in seawater. In Level 1 representing herbivory, Dunaliella salina microalgal culture pre-exposed to 13C-phenanthrene for 48 h was added to the coral treatment jars. In Level 2 representing predation, corals were provided a diet of copepod (Parvocalanus crassirostris) nauplii fed on D. salina pre-exposed to 13C-phenanthrene. Bioconcentration factors (BCF) and bioaccumulation factors (BAF) were calculated as appropriate for all organisms, and biomagnification factors (BMF) were calculated for A. millepora. We found that while phenanthrene uptake rates were not significantly different for the treatments, the accumulated concentration in corals was significantly higher in Level W (33.5 ± 2.83 mg kg-1) than in Level 1 (27.55 ± 2.77 mg kg-1) and Level 2 (29.36 ± 3.84 mg kg-1). Coral log BAF values increased with food-chain length; Level 2 log BAF (6.45) was higher than Level W log BCF (4.18) and Level 1 log BAF (4.5). Coral BMF was also higher for Level 2 than for Level 1. Exposure to dissolved or diet-bound phenanthrene had no significant effect on the coral symbionts' photosynthetic efficiency (Fv/Fm) as monitored by pulse-amplitude-modulation (PAM) fluorometry, indicating the PAH can be accumulated without toxic effects to their Photosystem II. Our study highlights the critical role of dietary exposure for pollutant accumulation in corals.

Cement and oil refining industries as the predominant sources of trace metal pollution in the Red Sea: A systematic study of element concentrations in the Red Sea zooplankton.

The Red Sea is exposed to metals from a large variety of natural and anthropogenic sources. In this study, we analyzed 19 common element concentrations in 14 Red Sea zooplankton samples using inductively coupled plasma-optical emission spectrometry (ICP-OES). The average metal or metalloid concentrations of the Red Sea zooplankton were: Ca > Sr > Fe > Al > Zn > As > Cu > Mn > Cr > Mo > Ni > Pb > Cd. The As, Ca, and Cu concentrations significantly increased with increasing latitude, while Cd concentrations decreased (p < 0.01). Our study indicated that anthropogenic activities (i.e., cement factories and oil refining industries) might be the predominant sources of significantly high Cr (1718 mg/kg), Fe (11,274 mg/kg), Mn (57.3 mg/kg), Mo (286 mg/kg), Ni (226 mg/kg), Pb (332 mg/kg), and Zn (17,046 mg/kg) concentrations that recorded in the Central to North Red Sea zooplankton.

Moderate Seasonal Dynamics Indicate an Important Role for Lysogeny in the Red Sea.

Viruses are the most abundant microorganisms in marine environments and viral infections can be either lytic (virulent) or lysogenic (temperate phage) within the host cell. The aim of this study was to quantify viral dynamics (abundance and infection) in the coastal Red Sea, a narrow oligotrophic basin with high surface water temperatures (22-32 °C degrees), high salinity (37.5-41) and continuous high insolation, thus making it a stable and relatively unexplored environment. We quantified viral and environmental changes in the Red Sea (two years) and the occurrence of lysogenic bacteria (induced by mitomycin C) on the second year. Water temperatures ranged from 24.0 to 32.5 °C, and total viral and bacterial abundances ranged from 1.5 to 8.7 × 106 viruses mL-1 and 1.9 to 3.2 × 105 bacteria mL-1, respectively. On average, 12.24% ± 4.8 (SE) of the prophage bacteria could be induced by mitomycin C, with the highest percentage of 55.8% observed in January 2018 when bacterial abundances were low; whereas no induction was measurable in spring when bacterial abundances were highest. Thus, despite the fact that the Red Sea might be perceived as stable, warm and saline, relatively modest changes in seasonal conditions were associated with large swings in the prevalence of lysogeny.

Assessment of Red Sea temperatures in CMIP5 models for present and future climate.

The increase of the temperature in the Red Sea basin due to global warming could have a large negative effect on its marine ecosystem. Consequently, there is a growing interest, from the scientific community and public organizations, in obtaining reliable projections of the Red Sea temperatures throughout the 21st century. However, the main tool used to do climate projections, the global climate models (GCM), may not be well suited for that relatively small region. In this work we assess the skills of the CMIP5 ensemble of GCMs in reproducing different aspects of the Red Sea 3D temperature variability. The results suggest that some of the GCMs are able to reproduce the present variability at large spatial scales with accuracy comparable to medium and high-resolution hindcasts. In general, the skills of the GCMs are better inside the Red Sea than outside, in the Gulf of Aden. Based on their performance, 8 of the original ensemble of 43 GCMs have been selected to project the temperature evolution of the basin. Bearing in mind the GCM limitations, this can be an useful benchmark once the high resolution projections are available. Those models project an averaged warming at the end of the century (2080-2100) of 3.3 ±> 0.6°C and 1.6 ±> 0.4°C at the surface under the scenarios RCP8.5 and RCP4.5, respectively. In the deeper layers the warming is projected to be smaller, reaching 2.2 ±> 0.5°C and 1.5 ±> 0.3°C at 300 m. The projected warming will largely overcome the natural multidecadal variability, which could induce temporary and moderate decrease of the temperatures but not enough to fully counteract it. We have also estimated how the rise of the mean temperature could modify the characteristics of the marine heatwaves in the region. The results show that the average length of the heatwaves would increase ~15 times and the intensity of the heatwaves ~4 times with respect to the present conditions under the scenario RCP8.5 (10 time and 3.6 times, respectively, under scenario RCP4.5).

Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities.

The deep sea, the largest ocean's compartment, drives planetary-scale biogeochemical cycling. Yet, the functional exploration of its microbial communities lags far behind other environments. Here we analyze 58 metagenomes from tropical and subtropical deep oceans to generate the Malaspina Gene Database. Free-living or particle-attached lifestyles drive functional differences in bathypelagic prokaryotic communities, regardless of their biogeography. Ammonia and CO oxidation pathways are enriched in the free-living microbial communities and dissimilatory nitrate reduction to ammonium and H2 oxidation pathways in the particle-attached, while the Calvin Benson-Bassham cycle is the most prevalent inorganic carbon fixation pathway in both size fractions. Reconstruction of the Malaspina Deep Metagenome-Assembled Genomes reveals unique non-cyanobacterial diazotrophic bacteria and chemolithoautotrophic prokaryotes. The widespread potential to grow both autotrophically and heterotrophically suggests that mixotrophy is an ecologically relevant trait in the deep ocean. These results expand our understanding of the functional microbial structure and metabolic capabilities of the largest Earth aquatic ecosystem.